Contacts of the strand formed by residues 79 - 84 (chain A) in PDB entry 5M5R
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 79 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A MET* 3.5 3.1 - - - +
74A ASN* 2.9 42.9 + - + +
77A SER* 2.9 21.4 + - - +
78A LYS* 1.3 76.3 - - - +
80A ILE* 1.3 59.5 + - - +
90A ILE* 3.8 26.5 - - + -
91A PHE 3.2 7.6 - - - +
92A ASN* 3.8 25.6 - - + +
99A MET* 6.1 1.3 - - + -
113A TRP* 4.5 11.7 - - + -
132A MET* 5.9 2.0 - - + -
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Residues in contact with ILE 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A CYS* 4.2 8.1 - - - -
50A VAL* 4.5 9.2 - - + -
52A ILE* 4.3 12.1 - - + -
71A ALA* 4.2 18.8 - - + -
72A ILE 3.8 13.0 - - - +
73A MET* 4.0 26.7 - - + -
78A LYS 4.2 0.4 - - - -
79A VAL* 1.3 73.5 - - - +
81A ALA* 1.3 68.9 + - - +
82A LEU* 3.8 23.3 - - + +
89A GLN 3.9 1.0 - - - +
90A ILE* 3.5 4.9 - - - +
91A PHE* 2.9 47.7 + - + +
93A ILE* 4.0 12.6 - - + -
5C LEU* 4.1 9.4 - - + -
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Residues in contact with ALA 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ALA* 3.4 4.9 - - - -
72A ILE* 3.0 47.1 + - + +
80A ILE* 1.3 73.8 - - - +
82A LEU* 1.3 61.3 + - - +
89A GLN 3.5 5.2 - - - -
90A ILE* 3.5 23.8 - - + -
111A TRP* 3.6 20.6 - - + -
113A TRP* 4.3 10.9 - - + +
119A VAL* 5.0 2.0 - - + -
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Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A VAL* 5.3 0.7 - - + -
66A ILE* 4.0 24.5 - - + -
68A ALA* 3.9 24.7 - - + -
70A SER 3.5 4.3 - - - -
71A ALA* 4.0 19.3 - - + -
80A ILE* 3.8 28.0 - - + +
81A ALA* 1.3 75.9 - - - +
83A LYS* 1.3 60.1 + - - +
89A GLN 2.9 33.9 + - - +
91A PHE* 3.8 28.9 - - + -
111A TRP* 3.5 7.4 - - - -
4C LEU* 3.6 16.1 - - + +
5C LEU* 4.1 11.2 - - + -
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Residues in contact with LYS 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ALA* 3.3 4.2 - - - +
69A ASP* 2.7 66.2 + - - +
70A SER* 3.2 15.7 + - - -
82A LEU* 1.3 75.8 - - - +
84A ALA* 1.3 55.8 + - - +
85A GLY 4.7 4.2 + - - +
87A THR 3.1 12.1 - - - +
88A LEU* 3.7 11.9 - - + -
108A VAL* 2.9 43.4 + - + +
109A THR* 4.6 5.9 + - - +
110A PHE* 4.9 4.3 - - - +
111A TRP* 3.6 44.4 - - + +
4C LEU* 3.9 4.7 - - - -
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Residues in contact with ALA 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A SER 3.9 19.5 - - - +
68A ALA* 4.5 0.9 - - - -
69A ASP* 3.7 7.0 - - - +
83A LYS* 1.3 75.2 - - - +
85A GLY* 1.3 59.9 + - - +
86A LYS 3.1 1.0 + - - -
87A THR* 3.0 32.8 + - - +
4C LEU* 3.9 16.4 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il